I use a Pelican case to transport on far or long trips. However I prefer to use individual soft shell cases for drone and remote in my backpack when I'm just out and about on the town.
I see. I don't use Litchi, but another app called Dronepan to take the photos. I've never used 2 nadirs before.
Here's a few things you can try to see if Hugin will stitch something:
1) What if you select only one of the nadirs.
2) Select only one row of photos.
3) Select two rows, then three...
What is Hugin not doing? It doesn't automatically stitch your photos after you select all your source photos. You have to press the "Align" button (step 2).
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